R package: simpleSingleCell
Chapter: Analyzing single-cell RNA-seq data containing UMI counts
# run only once
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install("SingleCellExperiment")
BiocManager::install("simpleSingleCell", version = "3.8")
BiocManager::install("scater")
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Amit Zeisel, Ana B. Muñoz Manchado, Peter Lönnerberg, Gioele La Manno, Simone Codeluppi, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz, Charlotte Rolny, Gonçalo Castelo-Branco, Jens Hjerling-Leffler and Sten Linnarsson
Science 347:1138-1142, 2015
sce object that contains count matrices and metadata## ByLibSize ByFeature BySpike Remaining
## 1 8 3 8 2989
# Gene abundance
# Normalization of cell-specific biases
# Modeling and removing technical noise
# Distribution of expression of most highly expressed genes
# Dimensionality reduction
# Graph-based clustering
## my.clusters
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
## 194 104 237 633 147 238 634 160 156 91 17 173 84 57 27 37
# Evaluating graph-based clustering
# Detecting subpopulation-specific marker genes
## DataFrame with 10 rows and 8 columns
## Top p.value FDR
## <integer> <numeric> <numeric>
## Snap25 1 1.07760786252372e-273 2.13765071688825e-269
## Stmn3 1 8.01751747584536e-239 7.95217470841747e-235
## Mllt11 1 3.58429115569114e-202 1.42203167310888e-198
## Gad1 1 1.52719585816084e-177 3.02949842383362e-174
## Atp1a3 1 5.02531526306102e-173 8.30726490611157e-170
## Celf4 1 1.85709125842012e-162 2.16700701725171e-159
## Gad2 1 2.34227647329593e-152 2.11198810912598e-149
## Rcan2 1 1.37388316275679e-92 2.99491431863808e-90
## Synpr 1 1.0227847880535e-65 8.34937524305225e-64
## Tspyl4 2 1.47394127859716e-155 1.5388722707122e-152
## logFC.2 logFC.3 logFC.4
## <numeric> <numeric> <numeric>
## Snap25 1.42027121155466 3.80074765847389 0.605025633438071
## Stmn3 1.95773993790992 4.33436131857807 0.190025402712248
## Mllt11 1.65026134005567 3.08053402764227 0.485210901310954
## Gad1 3.96850838614864 4.03241470752414 4.12496737409042
## Atp1a3 0.0608442678448413 3.27602693247929 0.201568491665177
## Celf4 0.518085570255083 2.72886122621097 0.54708311844668
## Gad2 3.50737849218741 3.67858313779067 3.79238727543879
## Rcan2 2.17016391558053 1.81756905217195 2.22661702113425
## Synpr 3.04399639667943 3.11252157099165 3.0631569369004
## Tspyl4 1.24441455287679 2.78590837300274 1.36491453676626
## logFC.5 logFC.6
## <numeric> <numeric>
## Snap25 0.628791789169103 -0.468427774667559
## Stmn3 1.03511245025969 -0.0939076782690842
## Mllt11 1.17528301247514 0.418382860258258
## Gad1 3.75237913044294 4.15245102170302
## Atp1a3 1.21412773443475 1.01986241645697
## Celf4 0.850310787576184 0.318147219022062
## Gad2 3.47741412338435 3.80697721719507
## Rcan2 1.55046954978362 1.19099658493111
## Synpr 2.6477236735327 2.85526954311159
## Tspyl4 1.55432426140375 1.5044419890837